GEAR

GEAR: GEnetic Analysis Repository
Contributed by geneticker: a geneticist and a hacker

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The general option to call gear is "java -jar gear.jar".
It is easy to define alias on your own computer in which you define "alias gear=java -jar /path/gear.jar ". /path/ is the location of gear.jar on your computer.

The following procedures have already been included into gear.

1. Naive imputation
2. Generate genetic relatedness scores
3. Fst
4. Haseman-Elston regression
5. Genetic relationship statistics (effective number of markers)
6. DNA Fingerprint
7. Projected PC
8. Profile scores
9. Simulation
   • Polygenic for quantitative traits
   • Polygenic traits simulation
   • Discordant nuclear family simulation
   • GWAS data simulation
10. Hong Lee's transformation for heritability
11. BLUP
12. Quick IBD
13. HE linkage
14. Data manager

15. Meta-analysis

    • Meta watchdog
    • LambdaMeta
    • sfst
    • Gmeta

16. High Performance Computing

Citation:
Chen G.B. (2014) Estimating heritability of complex traits from genome- wide association studies using IBS-based Haseman–Elston regression. Front. Genet. 5:107.